Merge pull request #123 from janpfeifer/jupytext

 Added Jupytext support and `ndlv` script for debugging cells.

Dockerfile

@@ -29,8 +29,8 @@ RUN apt-get install --yes --no-install-recommends git
 #######################################################################################################
 # Go and GoNB Libraries
 #######################################################################################################
-ENV GO_VERSION=1.22.2
-ENV GONB_VERSION="v0.10.1"
+ENV GO_VERSION=1.22.5
+ENV GONB_VERSION="v0.10.2"
 ENV GOROOT=/usr/local/go
 ENV GOPATH=/opt/go
 ENV PATH=$PATH:$GOROOT/bin:$GOPATH/bin

README.md

@@ -15,6 +15,9 @@
 
 <img align="right" width="480px" src="https://repository-images.githubusercontent.com/599714179/38d0328a-abdb-4f69-9617-6ef136390708">
 
+* **NEW**: Now supported by [Jupytext](https://github.com/mwouts/jupytext): it allows one to write the notebook as a normal.
+  Go file, and use [Jupytext](https://github.com/mwouts/jupytext) to convert to a notebook (with markdown support, etc). 
+  See [example](https://github.com/mwouts/jupytext/issues/1244#issuecomment-2202097837).
 * Auto-complete and contextual help while coding.
 * Rich content display: HTML, markdown (with latex), images, javascript, svg, videos, etc.
   * Widgets (sliders, buttons) support: interact using HTML elements. Create your own widgets!
@@ -26,6 +29,7 @@
   start up, since each cell is compiled.
 * Run cell's `Test*` and `Benchmark*` functions with `go test`, simply adding `%test` to cell.
 * Support for `go.mod` and `go.work`, to allow local development. Including importing specific versions of libraries.
+* Debug using [gdlv](https://github.com/aarzilli/gdlv), a GUI for the [delve](https://github.com/go-delve/delve) debugger (see %help).
 * Shell command executions with `!` -- handy at times, for instance to install packages.
 * Reported to work with Github Codespace, [VSCode](docs/VSCode.md), Binder, Google's Colab, etc.
 * Very well documented and supported.

cmd/nbexec/nbexec.go

@@ -5,6 +5,7 @@ import (
 	"flag"
 	"fmt"
 	"github.com/go-rod/rod"
+	"github.com/go-rod/rod/lib/launcher"
 	"github.com/go-rod/rod/lib/proto"
 	"github.com/janpfeifer/gonb/common"
 	"github.com/janpfeifer/must"
@@ -267,9 +268,17 @@ func startJupyterNotebook() {
 }
 
 // Notebook instrumenting using go-rod.
-
 func executeNotebook(url string, inputBoxes []string) {
-	page := rod.New().MustConnect().MustPage(url)
+	// Use system's Google Chrome is available, for sandboxing:
+	var controlURL string
+	chromePath, err := exec.LookPath("google-chrome")
+	if err == nil {
+		controlURL = launcher.New().Bin(chromePath).MustLaunch()
+	} else {
+		klog.Warningf("Using rod downloaded chromium, with --no-sandbox")
+		controlURL = launcher.New().NoSandbox(true).MustLaunch()
+	}
+	page := rod.New().ControlURL(controlURL).MustConnect().MustPage(url)
 	klog.V(1).Infof("Waiting for opening of page %q", url)
 	page.MustWaitStable()
 

cmd/ndlv/ndlv

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+# ndlv is a wrapper script that executes gdlv, a delve GUI, from inside a gonb notebook.
+# It will fail if not being executed by gonb, or if dlv and gdlv are not installed, or if no cell has
+# yet been executed to be debugged.
+
+if [[ "${GONB_TMP_DIR}" == "" ]] ; then
+  echo "No being executed from a gonb notebook cell, GONB_TMP_DIR not set." 1>&2
+  exit 1
+fi
+if [[ "$(which dlv)" == "" ]] ; then
+  echo "Can't find delve (dlv) debugger. See https://github.com/go-delve/delve/tree/master/Documentation/installation" 1>&2
+  exit 1
+fi
+if [[ "$(which gdlv)" == "" ]] ; then
+  echo "Can't find gdlv GUI for delve debugger. See https://github.com/aarzilli/gdlv" 1>&2
+  exit 1
+fi
+
+go_binary="$(basename "${GONB_TMP_DIR}")"
+cd "${GONB_TMP_DIR}" || ( echo "Can't cd to GONB_TMP_DIR=${GONB_TMP_DIR}" ; exit 1 )
+
+if [[ ! -e "${go_binary}" ]] ; then
+  echo "Cell binary is not available (${GONB_TMP_DIR}/${go_binary}) -- has cell already been executed ?" 1>&2
+  exit 1
+fi
+
+gdlv debug "${go_binary}"

docs/CHANGELOG.md

@@ -1,5 +1,19 @@
 # GoNB Changelog
 
+## 0.10.2, 2024/07/10 Added Jupytext support and `ndlv` script for debugging cells.
+
+* [Jupytext](https://jupytext.readthedocs.io/en/latest/) integration [#120](https://github.com/janpfeifer/gonb/discussions/120):
+  * Many thanks for [Marc Wouts](github.com/mwouts) for [adding support in Jupytext](https://github.com/mwouts/jupytext/releases/tag/v1.16.3), 
+    and @HaveF for the help and starting the topic.
+  * Handle special commands to be prefixed with `//gonb:` -- this allows special commands to be parseable Go code, and makes it easier for IDEs.
+  * Ignore `package` tag -- as opposed to raising an error: also to make easy on IDEs that may require a `package` tag.
+  * Added special variation: `%exec <function_name> <args...>` that creates a main function that calls `<function_name>`
+    and sets the program arguments (flags) to the given values.
+* Added `ndlv` wrapper script for starting [gdlv](https://github.com/aarzilli/gdlv) on cell binary.
+  * Many thanks for @HaveF for the help -- see [#122](https://github.com/janpfeifer/gonb/discussions/122)
+* Notebook testing: changed `nbexec` to use system's google-chrome if available (with sandbox), or let Rod download 
+  chromium, but then use with --no-sandbox (since there is no SUID on the binaries).
+
 ## 0.10.1, 2024/04/14 Added support for Apache ECharts
 
 * Interrupt and Shutdown:

docs/coverage.txt

@@ -9,7 +9,7 @@ github.com/janpfeifer/gonb/main.go						SetUpKlog					66.7%
 github.com/janpfeifer/gonb/cache/cache.go					New						75.0%
 github.com/janpfeifer/gonb/cache/cache.go					AssertNoError					50.0%
 github.com/janpfeifer/gonb/cache/cache.go					MustNew						100.0%
-github.com/janpfeifer/gonb/cache/cache.go					NewInTmp					72.7%
+github.com/janpfeifer/gonb/cache/cache.go					NewInTmp					68.2%
 github.com/janpfeifer/gonb/cache/cache.go					MustNewInTmp					100.0%
 github.com/janpfeifer/gonb/cache/cache.go					NewHidden					80.0%
 github.com/janpfeifer/gonb/cache/cache.go					MustNewHidden					100.0%
@@ -28,7 +28,7 @@ github.com/janpfeifer/gonb/cache/cache.go					CacheWith					91.7%
 github.com/janpfeifer/gonb/cache/cache.go					Cache						0.0%
 github.com/janpfeifer/gonb/cmd/nbexec/nbexec.go				main						72.2%
 github.com/janpfeifer/gonb/cmd/nbexec/nbexec.go				startJupyterNotebook				73.2%
-github.com/janpfeifer/gonb/cmd/nbexec/nbexec.go				executeNotebook					81.8%
+github.com/janpfeifer/gonb/cmd/nbexec/nbexec.go				executeNotebook					78.6%
 github.com/janpfeifer/gonb/cmd/nbexec/nbexec.go				checkForInputBoxes				95.7%
 github.com/janpfeifer/gonb/common/common.go					Panicf						0.0%
 github.com/janpfeifer/gonb/common/common.go					Pause						0.0%
@@ -165,9 +165,9 @@ github.com/janpfeifer/gonb/internal/comms/namedpipes.go			*State.ProgramUnsubscr
 github.com/janpfeifer/gonb/internal/comms/namedpipes.go			*State.deliverProgramSubscriptionsLocked	62.5%
 github.com/janpfeifer/gonb/internal/dispatcher/comms.go			handleComms					55.6%
 github.com/janpfeifer/gonb/internal/dispatcher/dispatcher.go		RunKernel					80.0%
-github.com/janpfeifer/gonb/internal/dispatcher/dispatcher.go		handleShellMsg					71.0%
+github.com/janpfeifer/gonb/internal/dispatcher/dispatcher.go		handleShellMsg					78.4%
 github.com/janpfeifer/gonb/internal/dispatcher/dispatcher.go		handleBusyMessage				47.8%
-github.com/janpfeifer/gonb/internal/dispatcher/dispatcher.go		handleShutdownRequest				83.3%
+github.com/janpfeifer/gonb/internal/dispatcher/dispatcher.go		handleShutdownRequest				84.6%
 github.com/janpfeifer/gonb/internal/dispatcher/dispatcher.go		handleExecuteRequest				87.5%
 github.com/janpfeifer/gonb/internal/dispatcher/dispatcher.go		HandleInspectRequest				0.0%
 github.com/janpfeifer/gonb/internal/dispatcher/dispatcher.go		handleCompleteRequest				0.0%
@@ -185,7 +185,7 @@ github.com/janpfeifer/gonb/internal/goexec/composer.go			*Declarations.RenderFun
 github.com/janpfeifer/gonb/internal/goexec/composer.go			*Declarations.RenderTypes			100.0%
 github.com/janpfeifer/gonb/internal/goexec/composer.go			*Declarations.RenderConstants			100.0%
 github.com/janpfeifer/gonb/internal/goexec/composer.go			*Constant.Render				100.0%
-github.com/janpfeifer/gonb/internal/goexec/composer.go			*State.createGoFileFromLines			85.7%
+github.com/janpfeifer/gonb/internal/goexec/composer.go			*State.createGoFileFromLines			81.8%
 github.com/janpfeifer/gonb/internal/goexec/composer.go			*State.createCodeFileFromDecls			58.8%
 github.com/janpfeifer/gonb/internal/goexec/composer.go			*State.createAlternativeFileFromDecls		0.0%
 github.com/janpfeifer/gonb/internal/goexec/composer.go			*State.createCodeFromDecls			71.9%
@@ -258,6 +258,7 @@ github.com/janpfeifer/gonb/internal/goexec/parser.go			*State.readMainGo				77.8
 github.com/janpfeifer/gonb/internal/goexec/parser.go			*State.SetCellTests				100.0%
 github.com/janpfeifer/gonb/internal/goexec/parser.go			*State.DefaultCellTestArgs			100.0%
 github.com/janpfeifer/gonb/internal/goexec/parser.go			IsEmptyLines					77.8%
+github.com/janpfeifer/gonb/internal/goexec/parser.go			TrimGonbCommentPrefix				100.0%
 github.com/janpfeifer/gonb/internal/goexec/tracking.go			newTrackingInfo					100.0%
 github.com/janpfeifer/gonb/internal/goexec/tracking.go			*State.Track					100.0%
 github.com/janpfeifer/gonb/internal/goexec/tracking.go			*State.lockedTrack				54.8%
@@ -344,10 +345,10 @@ github.com/janpfeifer/gonb/internal/kernel/kernel.go			*SyncSocket.RunLocked
 github.com/janpfeifer/gonb/internal/kernel/kernel.go			*Kernel.IsStopped				66.7%
 github.com/janpfeifer/gonb/internal/kernel/kernel.go			*Kernel.StoppedChan				100.0%
 github.com/janpfeifer/gonb/internal/kernel/kernel.go			*Kernel.Stop					72.2%
-github.com/janpfeifer/gonb/internal/kernel/kernel.go			*Kernel.HandleInterrupt				88.2%
+github.com/janpfeifer/gonb/internal/kernel/kernel.go			*Kernel.HandleInterrupt				58.8%
 github.com/janpfeifer/gonb/internal/kernel/kernel.go			*Kernel.SubscribeInterrupt			80.0%
 github.com/janpfeifer/gonb/internal/kernel/kernel.go			*Kernel.UnsubscribeInterrupt			75.0%
-github.com/janpfeifer/gonb/internal/kernel/kernel.go			*Kernel.callInterruptSubscribers		42.9%
+github.com/janpfeifer/gonb/internal/kernel/kernel.go			*Kernel.CallInterruptSubscribers		42.9%
 github.com/janpfeifer/gonb/internal/kernel/kernel.go			*Kernel.ExitWait				100.0%
 github.com/janpfeifer/gonb/internal/kernel/kernel.go			*Kernel.Stdin					100.0%
 github.com/janpfeifer/gonb/internal/kernel/kernel.go			*Kernel.Shell					100.0%
@@ -395,7 +396,7 @@ github.com/janpfeifer/gonb/internal/nbtests/nbtests.go			Sequence					63.2%
 github.com/janpfeifer/gonb/internal/nbtests/nbtests.go			OutputLine					100.0%
 github.com/janpfeifer/gonb/internal/nbtests/nbtests.go			InputLine					100.0%
 github.com/janpfeifer/gonb/internal/specialcmd/cellmagic.go			IsGoCell					0.0%
-github.com/janpfeifer/gonb/internal/specialcmd/cellmagic.go			ExecuteSpecialCell				80.0%
+github.com/janpfeifer/gonb/internal/specialcmd/cellmagic.go			ExecuteSpecialCell				81.0%
 github.com/janpfeifer/gonb/internal/specialcmd/cellmagic.go			cellCmdWritefile				87.5%
 github.com/janpfeifer/gonb/internal/specialcmd/cellmagic.go			writeLinesToFile				85.7%
 github.com/janpfeifer/gonb/internal/specialcmd/cellmagic.go		cellCmdScript					50.0%
@@ -404,9 +405,9 @@ github.com/janpfeifer/gonb/internal/specialcmd/definitions.go		displayEnumeratio
 github.com/janpfeifer/gonb/internal/specialcmd/definitions.go		listDefinitions					100.0%
 github.com/janpfeifer/gonb/internal/specialcmd/definitions.go		removeDefinitionImpl				87.5%
 github.com/janpfeifer/gonb/internal/specialcmd/definitions.go		removeDefinitions				75.0%
-github.com/janpfeifer/gonb/internal/specialcmd/specialcmd.go		Parse						84.0%
-github.com/janpfeifer/gonb/internal/specialcmd/specialcmd.go		joinLine					85.7%
-github.com/janpfeifer/gonb/internal/specialcmd/specialcmd.go		execSpecialConfig				54.4%
+github.com/janpfeifer/gonb/internal/specialcmd/specialcmd.go		Parse						84.6%
+github.com/janpfeifer/gonb/internal/specialcmd/specialcmd.go		joinLine					87.5%
+github.com/janpfeifer/gonb/internal/specialcmd/specialcmd.go		execSpecialConfig				55.3%
 github.com/janpfeifer/gonb/internal/specialcmd/specialcmd.go		execShell					100.0%
 github.com/janpfeifer/gonb/internal/specialcmd/specialcmd.go		splitCmd					97.0%
 github.com/janpfeifer/gonb/internal/specialcmd/track.go			execTrack					27.3%

examples/tests/bash_script.ipynb

@@ -34,7 +34,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "/tmp/gonb_9dda40ab\n"
+      "/tmp/gonb_af538290\n"
      ]
     }
    ],
@@ -59,7 +59,7 @@
      "output_type": "stream",
      "text": [
       "/home/janpf/Projects/gonb/examples/tests\n",
-      "/tmp/gonb_9dda40ab\n",
+      "/tmp/gonb_af538290\n",
       "/home/janpf/Projects/gonb\n",
       "/home/janpf/Projects/gonb\n"
      ]
@@ -86,7 +86,7 @@
    "name": "go",
    "nbconvert_exporter": "",
    "pygments_lexer": "",
-   "version": "go1.22.1"
+   "version": "go1.22.4"
   }
  },
  "nbformat": 4,

examples/tests/comms.ipynb

@@ -308,7 +308,7 @@
    "name": "go",
    "nbconvert_exporter": "",
    "pygments_lexer": "",
-   "version": "go1.22.1"
+   "version": "go1.22.4"
   }
  },
  "nbformat": 4,

examples/tests/dom.ipynb

@@ -88,7 +88,7 @@
     {
      "data": {
       "text/html": [
-       "<div id=\"dom.transient_div_86d0ec90\"></div>"
+       "<div id=\"dom.transient_div_88e9bcad\"></div>"
       ]
      },
      "metadata": {},
@@ -152,7 +152,7 @@
     {
      "data": {
       "text/html": [
-       "<div id=\"dom.transient_div_9113427e\"></div>"
+       "<div id=\"dom.transient_div_33dbca98\"></div>"
       ]
      },
      "metadata": {},
@@ -197,7 +197,7 @@
    "name": "go",
    "nbconvert_exporter": "",
    "pygments_lexer": "",
-   "version": "go1.22.0"
+   "version": "go1.22.4"
   }
  },
  "nbformat": 4,

examples/tests/functions.ipynb

@@ -65,7 +65,7 @@
    "name": "go",
    "nbconvert_exporter": "",
    "pygments_lexer": "",
-   "version": "go1.22.0"
+   "version": "go1.22.4"
   }
  },
  "nbformat": 4,

examples/tests/goflags.ipynb

@@ -153,9 +153,9 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "gonb_bc1385f7/main.go:8:\tA\t\t100.0%\n",
-      "gonb_bc1385f7/main.go:12:\tB\t\t0.0%\n",
-      "gonb_bc1385f7/main.go:17:\tmain\t\t100.0%\n",
+      "gonb_17c43c9d/main.go:8:\tA\t\t100.0%\n",
+      "gonb_17c43c9d/main.go:12:\tB\t\t0.0%\n",
+      "gonb_17c43c9d/main.go:17:\tmain\t\t100.0%\n",
       "total\t\t\t\t(statements)\t75.0%\n"
      ]
     }
@@ -238,14 +238,14 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "# gonb_bc1385f7\n",
+      "# gonb_17c43c9d\n",
       "./main.go:10:6: can inline (*Point).ManhattanLen\n",
       "./main.go:16:12: inlining call to flag.Parse\n",
-      "./main.go:18:28: inlining call to (*Point).ManhattanLen\n",
-      "./main.go:18:13: inlining call to fmt.Println\n",
+      "./main.go:18:27: inlining call to (*Point).ManhattanLen\n",
+      "./main.go:18:12: inlining call to fmt.Println\n",
       "./main.go:10:7: p does not escape\n",
-      "./main.go:18:13: ... argument does not escape\n",
-      "./main.go:18:28: ~r0 escapes to heap\n"
+      "./main.go:18:12: ... argument does not escape\n",
+      "./main.go:18:27: ~r0 escapes to heap\n"
      ]
     }
    ],
@@ -267,7 +267,7 @@
    "name": "go",
    "nbconvert_exporter": "",
    "pygments_lexer": "",
-   "version": "go1.22.0"
+   "version": "go1.22.4"
   }
  },
  "nbformat": 4,

examples/tests/gonbui.ipynb

@@ -22,7 +22,7 @@
      "output_type": "stream",
      "text": [
       "%goflags=[\"--cover\" \"--covermode=set\"]\n",
-      "GOCOVERDIR=/tmp/gonb_test_coverage.4mPvyGK2OJ\n"
+      "GOCOVERDIR=/tmp/gonb_test_coverage.9v84ceUYUN\n"
      ]
     }
    ],
@@ -133,7 +133,7 @@
    "name": "go",
    "nbconvert_exporter": "",
    "pygments_lexer": "",
-   "version": "go1.22.0"
+   "version": "go1.22.4"
   }
  },
  "nbformat": 4,

examples/tests/gotest.ipynb

@@ -287,12 +287,12 @@
      "text": [
       "goos: linux\n",
       "goarch: amd64\n",
-      "pkg: gonb_36f3efc5\n",
-      "cpu: Intel(R) Core(TM) i7-1065G7 CPU @ 1.30GHz\n",
+      "pkg: gonb_ce57b149\n",
+      "cpu: 12th Gen Intel(R) Core(TM) i9-12900K\n",
       "BenchmarkFibonacciA32\n",
-      "BenchmarkFibonacciA32-8   \t      50\t  22759741 ns/op\n",
+      "BenchmarkFibonacciA32-24    \t     177\t   6414568 ns/op\n",
       "BenchmarkFibonacciB32\n",
-      "BenchmarkFibonacciB32-8   \t28774705\t        39.85 ns/op\n",
+      "BenchmarkFibonacciB32-24    \t107397702\t        12.40 ns/op\n",
       "PASS\n",
       "coverage: [no statements]\n"
      ]
@@ -334,10 +334,10 @@
      "text": [
       "goos: linux\n",
       "goarch: amd64\n",
-      "pkg: gonb_36f3efc5\n",
-      "cpu: Intel(R) Core(TM) i7-1065G7 CPU @ 1.30GHz\n",
-      "BenchmarkFibonacciA32-8   \t      52\t  22831751 ns/op\n",
-      "BenchmarkFibonacciB32-8   \t31159093\t        40.49 ns/op\n",
+      "pkg: gonb_ce57b149\n",
+      "cpu: 12th Gen Intel(R) Core(TM) i9-12900K\n",
+      "BenchmarkFibonacciA32-24    \t     174\t   6429990 ns/op\n",
+      "BenchmarkFibonacciB32-24    \t100000000\t        11.82 ns/op\n",
       "PASS\n",
       "coverage: [no statements]\n"
      ]
@@ -361,7 +361,7 @@
    "name": "go",
    "nbconvert_exporter": "",
    "pygments_lexer": "",
-   "version": "go1.22.0"
+   "version": "go1.22.4"
   }
  },
  "nbformat": 4,